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Using small RNA-seq data to detect siRNA duplexes induced by plant viruses.

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Title Using small RNA-seq data to detect siRNA duplexes induced by plant viruses.
 
Creator Niu, X.
Sun, Y.
Chen, Z.
Li, R.
Padmanabhan, C.
Ruan, J.
Kreuze, J.F.
Ling, K.S.
Fei, Z.J.
Gao, S.
 
Subject RNA
VIROLOGY
PLANT VIRUSES
NUCLEOTIDE SEQUENCE
 
Description Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5'- and 3'-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining. The analytical results of the features in the detected siRNA duplexes were consistent with those from previous studies. The investigation of siRNA duplexes is useful for a better understanding of the RNA interference (RNAi) mechanism. It can also help to improve the virus detection based on the small RNA sequencing (sRNA-seq) technologies and to rationally design siRNAs for RNAi experiments.
Peer Review
 
Date 2017-07-07T13:36:50Z
2017-07-07T13:36:50Z
2017-06
 
Type Journal Article
 
Identifier Niu, X.; Sun, Y.; Chen, Z.; Li, R.; Padmanabhan, C.; Ruan, J.; Kreuze, J.F.; Ling, K.S.; Fei, Z.J.; Gao, S. 2017. Using small RNA-seq data to detect siRNA duplexes induced by plant viruses. Genes. (Switzerland). ISSN 2073-4425. 8(6):8 p.
2073-4425
https://hdl.handle.net/10568/82687
 
Language en
 
Format 8 p.
 
Source Genes